xyplot can't find channel (flowViz)
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ericjkort • 0
@ericjkort-7863
Last seen 6.4 years ago
United States

I am trying to use the xyplot to plot data from a single FCS (version 3) file, but receive an error that the markers cannot be found, despite the fact that I can find them using getChannelMarker.

>data <- read.FCS("test.FCS", column.pattern = "^[FS0-9][S0-9]")
>getChannelMarker(data, "FSC")
     name desc
$P11  FSC <NA>
>getChannelMarker(data, "SSC")
     name desc
$P13  SSC <NA>
>xyplot("FSC" ~ "SSC", data=data)
Error in getChannelMarker(frm, channel.x.name) : can't find "SSC"

The FCS file I am using can be downloaded from google drive here:

https://goo.gl/iYY6i3

I get the same error if I load the FCS file into a flowSet rather than a flowFrame.

Any insights into what I am doing wrong here?  Thank you!

-Eric


Here is my sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] flowViz_1.30.1  lattice_0.20-31 flowCore_1.32.2

loaded via a namespace (and not attached):
 [1] Biobase_2.26.0      BiocGenerics_0.12.1 cluster_2.0.2       corpcor_1.6.8       DEoptimR_1.0-2    
 [6] graph_1.44.1        grid_3.1.2          hexbin_1.27.0       IDPmisc_1.1.17      KernSmooth_2.23-15
[11] latticeExtra_0.6-26 MASS_7.3-42         mvtnorm_1.0-2       parallel_3.1.2      pcaPP_1.9-60      
[16] RColorBrewer_1.1-2  robustbase_0.92-4   rrcov_1.3-8         stats4_3.1.2        tools_3.1.2    
flowcore flowviz flowcytometry • 1.3k views
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Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 8 weeks ago
(Private Address)

You don't want the regular quote marks in the formula( type help(formula) for more details).

simply removing 'quotes' will do

xyplot(FSC ~ SSC, data)

Or quote it with backticks If you have special characters

xyplot(`FSC-A` ~ `SSC-A`, data)

 

Also, if you don't mind to endeavor  to use `dev` version, please check out 'ggcyto' package (https://github.com/RGLab/ggcyto), it uses `ggplot-like` syntax which is the de facto of trellis plotting nowadays)

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Perfect.  Thank you!

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